[2023-03-15 12:44:24,471] [INFO] DFAST_QC pipeline started.
[2023-03-15 12:44:24,472] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 12:44:24,472] [INFO] DQC Reference Directory: /var/lib/cwl/stg7337d43f-0398-416a-bc60-3f545d28ae1a/dqc_reference
[2023-03-15 12:44:26,210] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 12:44:26,210] [INFO] Task started: Prodigal
[2023-03-15 12:44:26,210] [INFO] Running command: cat /var/lib/cwl/stg706b6e61-9779-4f93-9b0c-24c5f5009669/OceanDNA-b27605.fa | prodigal -d OceanDNA-b27605/cds.fna -a OceanDNA-b27605/protein.faa -g 11 -q > /dev/null
[2023-03-15 12:44:43,892] [INFO] Task succeeded: Prodigal
[2023-03-15 12:44:43,892] [INFO] Task started: HMMsearch
[2023-03-15 12:44:43,893] [INFO] Running command: hmmsearch --tblout OceanDNA-b27605/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7337d43f-0398-416a-bc60-3f545d28ae1a/dqc_reference/reference_markers.hmm OceanDNA-b27605/protein.faa > /dev/null
[2023-03-15 12:44:44,130] [INFO] Task succeeded: HMMsearch
[2023-03-15 12:44:44,130] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg706b6e61-9779-4f93-9b0c-24c5f5009669/OceanDNA-b27605.fa]
[2023-03-15 12:44:44,150] [INFO] Query marker FASTA was written to OceanDNA-b27605/markers.fasta
[2023-03-15 12:44:44,150] [INFO] Task started: Blastn
[2023-03-15 12:44:44,150] [INFO] Running command: blastn -query OceanDNA-b27605/markers.fasta -db /var/lib/cwl/stg7337d43f-0398-416a-bc60-3f545d28ae1a/dqc_reference/reference_markers.fasta -out OceanDNA-b27605/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 12:44:44,758] [INFO] Task succeeded: Blastn
[2023-03-15 12:44:44,758] [INFO] Selected 22 target genomes.
[2023-03-15 12:44:44,759] [INFO] Target genome list was writen to OceanDNA-b27605/target_genomes.txt
[2023-03-15 12:44:44,771] [INFO] Task started: fastANI
[2023-03-15 12:44:44,772] [INFO] Running command: fastANI --query /var/lib/cwl/stg706b6e61-9779-4f93-9b0c-24c5f5009669/OceanDNA-b27605.fa --refList OceanDNA-b27605/target_genomes.txt --output OceanDNA-b27605/fastani_result.tsv --threads 1
[2023-03-15 12:45:00,492] [INFO] Task succeeded: fastANI
[2023-03-15 12:45:00,493] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7337d43f-0398-416a-bc60-3f545d28ae1a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 12:45:00,493] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7337d43f-0398-416a-bc60-3f545d28ae1a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 12:45:00,505] [INFO] Found 22 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 12:45:00,505] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 12:45:00,506] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Aestuariivita boseongensis	strain=BS-B2	GCA_001262635.1	1470562	1470562	type	True	82.7829	686	919	95	below_threshold
Antarcticimicrobium luteum	strain=318-1	GCA_004358185.1	2547397	2547397	type	True	77.6029	311	919	95	below_threshold
Ruegeria intermedia	strain=DSM 29341	GCA_900129345.1	996115	996115	type	True	77.5968	298	919	95	below_threshold
Cribrihabitans marinus	strain=DSM 29340	GCA_900109035.1	1227549	1227549	type	True	77.2663	289	919	95	below_threshold
Roseovarius atlanticus	strain=R12B	GCA_001441615.1	1641875	1641875	type	True	77.2531	218	919	95	below_threshold
Cribrihabitans marinus	strain=CGMCC 1.13219	GCA_014640375.1	1227549	1227549	type	True	77.2311	292	919	95	below_threshold
Leisingera methylohalidivorans	strain=DSM 14336; MB2	GCA_000511355.1	133924	133924	type	True	77.2101	233	919	95	below_threshold
Roseovarius indicus	strain=DSM 26383	GCA_900112725.1	540747	540747	type	True	77.1326	215	919	95	below_threshold
Salipiger marinus	strain=DSM 26424	GCA_900100085.1	555512	555512	type	True	77.1063	235	919	95	below_threshold
Roseovarius indicus	strain=B108	GCA_001441635.1	540747	540747	type	True	77.0872	217	919	95	below_threshold
Roseovarius indicus	strain=DSM 26383	GCA_008728195.1	540747	540747	type	True	77.0228	220	919	95	below_threshold
Lutimaribacter saemankumensis	strain=DSM 28010	GCA_900100005.1	490829	490829	type	True	76.9996	255	919	95	below_threshold
Leisingera daeponensis	strain=DSM 23529	GCA_000473145.1	405746	405746	type	True	76.9614	282	919	95	below_threshold
Roseovarius halotolerans	strain=DSM 29507	GCA_003634925.1	505353	505353	type	True	76.9598	184	919	95	below_threshold
Roseovarius confluentis	strain=SAG6	GCA_002917925.1	1852027	1852027	type	True	76.8483	214	919	95	below_threshold
Pelagivirga sediminicola	strain=BH-SD19	GCA_003072125.1	2170575	2170575	type	True	76.7172	197	919	95	below_threshold
Pelagivirga dicentrarchi	strain=YLY04	GCA_003316635.1	2250573	2250573	type	True	76.6242	173	919	95	below_threshold
Rhabdonatronobacter sediminivivens	strain=IM2376	GCA_013415485.1	2743469	2743469	type	True	76.5613	147	919	95	below_threshold
Salinihabitans flavidus	strain=DSM 27842	GCA_900110425.1	569882	569882	type	True	76.4874	180	919	95	below_threshold
Pseudophaeobacter flagellatus	strain=MA21411-1	GCA_021228235.1	2899119	2899119	type	True	76.264	184	919	95	below_threshold
Salipiger pallidus	strain=CGMCC 1.15762	GCA_014643635.1	1775170	1775170	type	True	76.2421	131	919	95	below_threshold
Marivivens aquimaris	strain=GSB7	GCA_015220045.1	2774876	2774876	type	True	76.1279	83	919	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 12:45:00,506] [INFO] DFAST Taxonomy check result was written to OceanDNA-b27605/tc_result.tsv
[2023-03-15 12:45:00,506] [INFO] ===== Taxonomy check completed =====
[2023-03-15 12:45:00,506] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 12:45:00,506] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7337d43f-0398-416a-bc60-3f545d28ae1a/dqc_reference/checkm_data
[2023-03-15 12:45:00,507] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 12:45:00,532] [INFO] Task started: CheckM
[2023-03-15 12:45:00,533] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b27605/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b27605/checkm_input OceanDNA-b27605/checkm_result
[2023-03-15 12:45:46,737] [INFO] Task succeeded: CheckM
[2023-03-15 12:45:46,738] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 66.32%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 12:45:46,740] [INFO] ===== Completeness check finished =====
[2023-03-15 12:45:46,740] [INFO] ===== Start GTDB Search =====
[2023-03-15 12:45:46,740] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b27605/markers.fasta)
[2023-03-15 12:45:46,742] [INFO] Task started: Blastn
[2023-03-15 12:45:46,742] [INFO] Running command: blastn -query OceanDNA-b27605/markers.fasta -db /var/lib/cwl/stg7337d43f-0398-416a-bc60-3f545d28ae1a/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b27605/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 12:45:47,669] [INFO] Task succeeded: Blastn
[2023-03-15 12:45:47,670] [INFO] Selected 19 target genomes.
[2023-03-15 12:45:47,670] [INFO] Target genome list was writen to OceanDNA-b27605/target_genomes_gtdb.txt
[2023-03-15 12:45:47,749] [INFO] Task started: fastANI
[2023-03-15 12:45:47,750] [INFO] Running command: fastANI --query /var/lib/cwl/stg706b6e61-9779-4f93-9b0c-24c5f5009669/OceanDNA-b27605.fa --refList OceanDNA-b27605/target_genomes_gtdb.txt --output OceanDNA-b27605/fastani_result_gtdb.tsv --threads 1
[2023-03-15 12:46:01,141] [INFO] Task succeeded: fastANI
[2023-03-15 12:46:01,153] [INFO] Found 19 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 12:46:01,153] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCF_001262635.1	s__Aestuariivita boseongensis	82.7937	686	919	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Aestuariivita	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018401465.1	s__Aestuariivita sp018401465	77.9791	362	919	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Aestuariivita	95.0	N/A	N/A	N/A	N/A	1	-
GCA_006227805.1	s__Aestuariivita sp006227805	77.7979	272	919	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Aestuariivita	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000161775.1	s__Ruegeria lacuscaerulensis	77.5178	293	919	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	99.98	99.98	1.00	1.00	2	-
GCF_013030985.1	s__Ruegeria arenilitoris_B	77.2765	247	919	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	99.15	99.15	0.92	0.92	2	-
GCF_900109035.1	s__Cribrihabitans marinus	77.2472	291	919	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cribrihabitans	95.0	100.00	100.00	0.99	0.99	2	-
GCA_003217735.2	s__Marinibacterium sp003217735	77.1342	279	919	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marinibacterium	95.0	98.81	98.75	0.89	0.89	3	-
GCF_900108275.1	s__Jhaorihella thermophila	77.0816	259	919	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Jhaorihella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013032025.1	s__Ruegeria atlantica_C	77.0622	196	919	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	100.00	100.00	0.99	0.99	2	-
GCA_003511785.1	s__UBA7951 sp003511785	77.0464	204	919	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__UBA7951	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008728195.1	s__Roseovarius indicus	77.046	218	919	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	99.18	97.54	0.97	0.92	4	-
GCF_900100005.1	s__Lutimaribacter saemankumensis	77.01	254	919	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Lutimaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013377785.1	s__Ruegeria haliotis	76.9649	190	919	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900172255.1	s__Roseovarius halotolerans	76.8999	186	919	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	100.00	100.00	1.00	1.00	2	-
GCF_009363655.1	s__Roseovarius sp009363655	76.8669	240	919	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	98.13	98.13	0.93	0.93	2	-
GCF_002917925.1	s__Roseovarius confluentis	76.8488	214	919	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	98.93	98.93	0.93	0.93	2	-
GCF_013035315.1	s__Ruegeria arenilitoris_D	76.756	207	919	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	95.80	95.80	0.90	0.90	2	-
GCF_003316635.1	s__Roseovarius dicentrarchi	76.6242	173	919	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900110425.1	s__Salinihabitans flavidus	76.4874	180	919	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salinihabitans	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 12:46:01,153] [INFO] GTDB search result was written to OceanDNA-b27605/result_gtdb.tsv
[2023-03-15 12:46:01,154] [INFO] ===== GTDB Search completed =====
[2023-03-15 12:46:01,156] [INFO] DFAST_QC result json was written to OceanDNA-b27605/dqc_result.json
[2023-03-15 12:46:01,156] [INFO] DFAST_QC completed!
[2023-03-15 12:46:01,156] [INFO] Total running time: 0h1m37s